5X06 | pdb_00005x06

DNA replication regulation protein

PDB DOI: https://doi.org/10.2210/pdb5X06/pdb

Classification: REPLICATION
Organism(s): Escherichia coli O157:H7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-01-20 Released: 2018-01-24
Deposition Author(s): Kim, J., Cho, Y.
Funding Organization(s): National Research Foundation of Korea funded by the Korea Government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free:
0.265 (Depositor), 0.273 (DCC)
R-Value Work:
0.226 (Depositor), 0.229 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Replication regulation protein

Kim, J., Cho, Y.

To be published.

Macromolecule Content

Total Structure Weight: 288.72 kDa
Atom Count: 18,264
Modeled Residue Count: 2,300
Deposited Residue Count: 2,556
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit beta	A, B, C, D	386	Escherichia coli O157:H7	Mutation(s): 0 Gene Names: dnaN, Z5192, ECs4636 EC: 2.7.7.7
UniProt
Find proteins for P0A988 (Escherichia coli (strain K12)) Explore P0A988 Go to UniProtKB: P0A988
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A988
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DnaA regulatory inactivator Hda	E, F, G, H	253	Escherichia coli O157:H7	Mutation(s): 0 Gene Names: hda, Z3759, ECs3358
UniProt
Find proteins for P69931 (Escherichia coli (strain K12)) Explore P69931 Go to UniProtKB: P69931
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69931
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain P [auth G] SDF format, chain S [auth H] SDF format, chain N [auth F] MOL2 format, chain K [auth E] MOL2 format, chain P [auth G] MOL2 format, chain S [auth H] MOL2 format, chain N [auth F] mmCIF format, chain K [auth E] mmCIF format, chain P [auth G] mmCIF format, chain S [auth H] mmCIF format, chain N [auth F]	K [auth E], N [auth F], P [auth G], S [auth H]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth E] Focus chain N [auth F] Focus chain P [auth G] Focus chain S [auth H] Interactions & Density Focus chain K [auth E] Focus chain N [auth F] Focus chain P [auth G] Focus chain S [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth D] SDF format, chain M [auth E] SDF format, chain R [auth G] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] MOL2 format, chain M [auth E] MOL2 format, chain R [auth G] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D] mmCIF format, chain M [auth E] mmCIF format, chain R [auth G]	I [auth C], J [auth D], M [auth E], R [auth G]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth D] Focus chain M [auth E] Focus chain R [auth G] Interactions & Density Focus chain I [auth C] Focus chain J [auth D] Focus chain M [auth E] Focus chain R [auth G]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain Q [auth G] SDF format, chain T [auth H] SDF format, chain O [auth F] MOL2 format, chain L [auth E] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth H] MOL2 format, chain O [auth F] mmCIF format, chain L [auth E] mmCIF format, chain Q [auth G] mmCIF format, chain T [auth H] mmCIF format, chain O [auth F]	L [auth E], O [auth F], Q [auth G], T [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth E] Focus chain O [auth F] Focus chain Q [auth G] Focus chain T [auth H] Interactions & Density Focus chain L [auth E] Focus chain O [auth F] Focus chain Q [auth G] Focus chain T [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.24 Å
R-Value Free: 0.265 (Depositor), 0.273 (DCC)
R-Value Work: 0.226 (Depositor), 0.229 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.112	α = 90
b = 149.542	β = 90
c = 200.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-01-24

Deposition Author(s):

Kim, J.

Cho, Y.

Funding Organization	Location	Grant Number
National Research Foundation of Korea funded by the Korea Government	Korea, Republic Of	NRF-2015R1A2A1A05001694
National Research Foundation of Korea funded by the Korea Government	Korea, Republic Of	2012054226
National Research Foundation of Korea funded by the Korea Government	Korea, Republic Of	20120008833

Revision History (Full details and data files)

Version 1.0: 2018-01-24
Type: Initial release
Version 1.1: 2023-11-22
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description